Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems

Environmental Microbiome

Research

Dong Wang¹  Osama Abdalla Abdelshafy Mohamad²  Shuang Wang³  Lan Liu⁴  Ling-Yu Zhang⁴  Ming-Xian Han⁴  Wen-Hui Lian⁴  Shuai Li⁴  Lei Dong⁴  Jian-Yu Jiao⁴  Wen-Jun Li⁵  Bao-Zhu Fang⁶  André Antunes⁷ 

[1] College of Life Science and Technology, Honghe University, 661199, Mengzi, People’s Republic of China;Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, 45511, Arish, Egypt;State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People’s Republic of China;Heilongjiang Academy of Black Soil Conservation and Utilization, 150086, Harbin, People’s Republic of China;State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People’s Republic of China;State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, People’s Republic of China;State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Urumqi, People’s Republic of China;State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Urumqi, People’s Republic of China;State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People’s Republic of China;

关键词: Culturomics;    Metagenomics;    Desert farming systems;    Rhizosphere microbiome;   

DOI  :  10.1186/s40793-023-00463-3

 received in 2022-05-20, accepted in 2023-01-08,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThe microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants.ResultsThe results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different.ConclusionHere, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.

【 授权许可】

CC BY   
© The Author(s) 2023

【 图 表 】

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